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  • 1
    Electronic Resource
    Electronic Resource
    Structural features are as important as sequence homologies inDrosophila heat shock gene upstream regions (1984)
    Springer
    Journal of molecular evolution 20 (1984), S. 106-110 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila heat shock ; Protein genes ; Structural homology ; Regulatory regions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Pelham has shown that theDrosophila hsp 70 gene is not transcribed under heat shock conditions unless a given upstream region is present. Davidson et al. have recently compiled a list of sequences homologous to this region in otherDrosophila heat shock genes. They proposed that a set of unlinked genes, such as the heat shock genes, could be coordinately induced through an interaction in cis with a common regulatory molecule. That this interaction involves structural elements is suggested by the fact that these upstream regions share inverted repeats as well as areas of Z-DNA potential. Furthermore, using the Calladine-Dickerson rules for local helical parameters, we show that these regions share structural homology. This is significant because the presence of regions homologous to a derived consensus sequence does not necessarily imply structural similarity. Therefore, we suggest that these structural features are at least as important as the sequence homologies in enabling the heat shock response.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02257370
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 259-266 
    Details
    ISSN: 1432-1432
    Keywords: DNA sequence analysis ; Frequencies ; Sequence patterns ; DNA structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The eukaryotic and prokaryotic databases are scanned for potential nearest-neighbor doublet preferences at the 5′ and 3′ flanks of some oligomers. Here we focus on oligomers containing alternating nucleotides, i.e., UV, UVUV, and UUVV where U≠V. Strong, consistent trends are observed in eukaryotic sequences. A/T alternation oligomers are preferentially flanked by A/T. G/C flanks are disfavored. G/C alternation oligomers are preferentially flanked by G/C. A/T flanks are disfavored. These trends are consistent with those observed previously for homooligomer tracts (Nussinov et al. 1989a,b). G/C tracts are preferentially flanked by G/C. A/T nearest neighbors are disfavored. The reverse holds for A/T tracts. Additional patterns are described here as well. The possible origin of these DNA composition and sequence trends is discussed. These trends are suggested to stem from protein-DNA interaction constraints.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100677
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Strong doublet preferences in nucleotide sequences and DNA geometry (1984)
    Springer
    Journal of molecular evolution 20 (1984), S. 111-119 
    Details
    ISSN: 1432-1432
    Keywords: Dinucleotides ; Sequence data ; DNA structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Analysis of the sequence data available today, comprising more than 500,000 bases, confirms the previously observed phenomenon that there are distinct dinucleotide preferences in DNA sequences. Consistent behaviour is observed in the major sequence groups analysed here in prokaryotes, eukaryotes and mitochondria. Some doublet preferences are common to all groups and are found in most sequences of the Los Alamos Library. The patterns seen in such large data sets are very significant statistically and biologically. Since they are present in numerous and diverse nucleotide sequences, one may conclude that they confer evolutionary advantages on the organism. In eukaryotes RR and YY dinucleotides are preferred over YR and RY (where R is a purine and Y a pyrimidine). Since opposite-chain nearest-neighbour purine clashes are major determinants of DNA structure, it appears that the tight packaging of DNA in nucleosomes disfavors, in general, such (YR and RY) steric repulsion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02257371
    Library Location Call Number Volume/Issue/Year Availability
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    Paper (German National Licenses)
    Fulltext
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